phonopy 3.2.0__tar.gz → 3.3.0__tar.gz

{phonopy-3.2.0 → phonopy-3.3.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: phonopy
-Version: 3.2.0
+Version: 3.3.0
 Summary: This is the phonopy module.
 Author-Email: Atsushi Togo <atz.togo@gmail.com>
 License-Expression: BSD-3-Clause

phonopy-3.3.0/phonopy/_version.py

@@ -0,0 +1,24 @@
+# file generated by vcs-versioning
+# don't change, don't track in version control
+from __future__ import annotations
+
+__all__ = [
+    "__version__",
+    "__version_tuple__",
+    "version",
+    "version_tuple",
+    "__commit_id__",
+    "commit_id",
+]
+
+version: str
+__version__: str
+__version_tuple__: tuple[int | str, ...]
+version_tuple: tuple[int | str, ...]
+commit_id: str | None
+__commit_id__: str | None
+
+__version__ = version = '3.3.0'
+__version_tuple__ = version_tuple = (3, 3, 0)
+
+__commit_id__ = commit_id = 'g9532062a8'

{phonopy-3.2.0 → phonopy-3.3.0}/phonopy/api_phonopy.py

@@ -256,7 +256,7 @@ class Phonopy:
         self._search_primitive_symmetry()
 
         # displacements
-        self._dataset = None
+        self._dataset: DisplacementDataset | None = None
         self._supercells_with_displacements = None
 
         # set_force_constants or set_forces
@@ -270,7 +270,7 @@ class Phonopy:
 
         # MLP
         self._mlp = None
-        self._mlp_dataset = None
+        self._mlp_dataset: Type2DisplacementDataset | None = None
 
         self._band_structure = None
         self._mesh = None
@@ -404,13 +404,13 @@ class Phonopy:
         return self._calculator
 
     @property
-    def dataset(self) -> dict | None:
+    def dataset(self) -> DisplacementDataset | None:
         """Return displacement-force dataset.
 
         Dataset containing information of displacements in supercells.
         This optionally contains energies and forces of respective supercells.
 
-        dataset : dict
+        dataset : DisplacementDataset or None
             The format can be either one of two types
 
             Type 1. One atomic displacement in each supercell:
@@ -441,13 +441,13 @@ class Phonopy:
         return self._dataset
 
     @dataset.setter
-    def dataset(self, dataset: dict | None) -> None:
+    def dataset(self, dataset: DisplacementDataset | None) -> None:
         if dataset is None:
             self._dataset = None
         elif "first_atoms" in dataset:
             self._dataset = copy.deepcopy(dataset)
         elif "displacements" in dataset:
-            self._dataset = {}
+            self._dataset = None
             self.displacements = dataset["displacements"]
             if "forces" in dataset:
                 self.forces = dataset["forces"]
@@ -552,14 +552,11 @@ class Phonopy:
         disp = np.array(displacements, dtype="double", order="C")
         if disp.ndim != 3 or disp.shape[1:] != (len(self._supercell), 3):
             raise RuntimeError("Array shape of displacements is incorrect.")
-        if self._dataset is None:
-            self._dataset = {}
-        if "first_atoms" in self._dataset:
+        if self._dataset is not None and "first_atoms" in self._dataset:
             raise RuntimeError(
                 "Setting displacements to type-1 dataset is not supported."
             )
-
-        self._dataset["displacements"] = disp
+        self._dataset = {"displacements": disp}
         self._supercells_with_displacements = None
 
     @property
@@ -3285,8 +3282,7 @@ class Phonopy:
             phpy_yaml = PhonopyYaml(
                 configuration=configuration, physical_units=units, settings=settings
             )
-        phpy_yaml.frequency_unit_conversion_factor = self._unit_conversion_factor
-        set_yaml(phpy_yaml, self)
+        set_data_to_phonopy_yaml(phpy_yaml, self)
         return phpy_yaml
 
     ###################
@@ -3528,8 +3524,8 @@ class Phonopy:
         """
         if self._dataset is None:
             raise RuntimeError("Displacement-force dataset is not set.")
-        if target in self._dataset:  # type-2
-            return self._dataset[target]
+        if "displacements" in self._dataset and target in self._dataset:  # type-2
+            return self._dataset[target]  # type: ignore
         if "first_atoms" in self._dataset:  # type-1
             values = []
             for disp in self._dataset["first_atoms"]:
@@ -3545,18 +3541,19 @@ class Phonopy:
 
     def _set_forces_energies(
         self,
-        values: NDArray[np.double]
+        values: Sequence[float]
+        | NDArray[np.double]
         | Sequence[NDArray[np.double]]
         | Sequence[Sequence[Sequence[float]]],
         target: Literal["forces", "supercell_energies"],
     ) -> None:
         assert self._dataset is not None
         if "first_atoms" in self._dataset:  # type-1
-            for disp, v in zip(self._dataset["first_atoms"], values, strict=True):  # type: ignore
+            for disp, val in zip(self._dataset["first_atoms"], values, strict=True):  # type: ignore
                 if target == "forces":
-                    disp[target] = np.array(v, dtype="double", order="C")
+                    disp[target] = np.array(val, dtype="double", order="C")
                 elif target == "supercell_energies":
-                    disp["supercell_energy"] = float(v)
+                    disp["supercell_energy"] = float(val)  # type: ignore
         elif "displacements" in self._dataset:  # type-2
             _values = np.array(values, dtype="double", order="C")
             natom = len(self._supercell)
@@ -3573,7 +3570,7 @@ class Phonopy:
             raise RuntimeError("Set of displacements is not available.")
 
 
-def set_yaml(phpy_yaml: PhonopyYaml, self: Phonopy) -> None:
+def set_data_to_phonopy_yaml(phpy_yaml: PhonopyYaml, self: Phonopy) -> None:
     """Set data to PhonopyYaml instance."""
     phpy_yaml.unitcell = self.unitcell
     phpy_yaml.primitive = self.primitive

{phonopy-3.2.0 → phonopy-3.3.0}/phonopy/harmonic/displacement.py

@@ -78,7 +78,7 @@ class FirstAtomDisplacement(TypedDict):
     """Displacement information of one displaced atom."""
 
     number: int
-    displacement: list[float]
+    displacement: NDArray[np.double]
 
 
 class FirstAtomDisplacementWithForces(FirstAtomDisplacement, total=False):

{phonopy-3.2.0 → phonopy-3.3.0}/phonopy/harmonic/force_constants.py

@@ -41,6 +41,7 @@ from collections.abc import Sequence
 import numpy as np
 from numpy.typing import NDArray
 
+from phonopy.harmonic.displacement import Type1DisplacementDataset
 from phonopy.structure.atoms import PhonopyAtoms
 from phonopy.structure.cells import (
     Primitive,
@@ -64,7 +65,7 @@ class FDFCSolver:
         supercell: PhonopyAtoms,
         primitive: Primitive | None,
         symmetry: Symmetry,
-        dataset: dict,
+        dataset: Type1DisplacementDataset,
         is_compact_fc: bool = False,
         log_level: int = 0,  # currently not used
     ):
@@ -93,7 +94,7 @@ class FDFCSolver:
         self,
         supercell: PhonopyAtoms,
         symmetry: Symmetry,
-        dataset: dict,
+        dataset: Type1DisplacementDataset,
         atom_list: NDArray[np.int64] | None = None,
         primitive: Primitive | None = None,
     ) -> NDArray[np.double]:
@@ -830,7 +831,7 @@ def _solve_force_constants_svd(
 def _get_force_constants_disps(
     force_constants: NDArray[np.double],
     supercell: PhonopyAtoms,
-    dataset: dict,
+    dataset: Type1DisplacementDataset,
     symmetry: Symmetry,
     atom_list: NDArray[np.int64] | None = None,
 ) -> NDArray[np.int64]:
@@ -861,11 +862,12 @@ def _get_force_constants_disps(
         disps = []
         sets_of_forces = []
 
-        for x in dataset["first_atoms"]:
-            if x["number"] != disp_atom_number:
+        for data_1st in dataset["first_atoms"]:
+            if data_1st["number"] != disp_atom_number:
                 continue
-            disps.append(x["displacement"])
-            sets_of_forces.append(x["forces"])
+            disps.append(data_1st["displacement"])
+            assert "forces" in data_1st
+            sets_of_forces.append(data_1st["forces"])
 
         site_symmetry = symmetry.get_site_symmetry(disp_atom_number)
 

{phonopy-3.2.0 → phonopy-3.3.0}/phonopy/interface/fc_calculator.py

@@ -46,6 +46,7 @@ from phonopy.exception import (
     ForceCalculatorRequiredError,
     ForceConstantsCalculatorNotFoundError,
 )
+from phonopy.harmonic.displacement import DisplacementDataset
 from phonopy.harmonic.force_constants import FDFCSolver
 from phonopy.interface.alm import ALMFCSolver
 from phonopy.interface.symfc import SymfcFCSolver, parse_symfc_options
@@ -77,7 +78,7 @@ def check_and_cast_fc_calculator_name(
 
 def get_fc_solver(
     supercell: PhonopyAtoms,
-    dataset: dict,
+    dataset: DisplacementDataset,
     primitive: Primitive | None = None,
     fc_calculator: Literal["traditional", "symfc", "alm"] | None = None,
     fc_calculator_options: str | None = None,
@@ -92,7 +93,7 @@ def get_fc_solver(
     ----------
     supercell : PhonopyAtoms
         Supercell
-    dataset : dict
+    dataset : DisplacementDataset
         Dataset that contains displacements, forces, and optionally energies.
     primitive : Primitive
         Primitive cell. Only needed for the traditional FC calculator.
@@ -135,7 +136,7 @@ def get_fc_solver(
 
 def get_fc2(
     supercell: PhonopyAtoms,
-    dataset: dict,
+    dataset: DisplacementDataset,
     primitive: Primitive | None = None,
     fc_calculator: Literal["traditional", "symfc", "alm"] | None = None,
     fc_calculator_options: str | None = None,
@@ -152,7 +153,7 @@ def get_fc2(
     ----------
     supercell : PhonopyAtoms
         Supercell
-    dataset : dict
+    dataset : DisplacementDataset
         Dataset that contains displacements, forces, and optionally energies.
     primitive : Primitive
         Primitive cell. Only needed for the traditional FC calculator.
@@ -199,7 +200,7 @@ class FCSolver:
         fc_solver_name: Literal["traditional", "symfc", "alm"],
         supercell: PhonopyAtoms,
         symmetry: Symmetry | None = None,
-        dataset: dict | None = None,
+        dataset: DisplacementDataset | None = None,
         is_compact_fc: bool = False,
         primitive: Primitive | None = None,
         orders: Sequence[int] | None = None,
@@ -222,7 +223,7 @@ class FCSolver:
             Supercell.
         symmetry : Symmetry, optional
             Symmetry of supercell. Default is None.
-        dataset : dict, optional
+        dataset : DisplacementDataset, optional
             Dataset that contains displacements, forces, and optionally
             energies. Default is None.
         is_compact_fc : bool, optional

{phonopy-3.2.0 → phonopy-3.3.0}/phonopy/interface/phonopy_yaml.py

@@ -651,17 +651,11 @@ class PhonopyYamlDumperBase(ABC):
         dataset: DisplacementDataset | None,
         with_forces: bool = False,
         key_prefix: str = "",
-        v223_mode: bool = False,
     ) -> list[str]:
         """Choose yaml writer depending on the dataset type.
 
         See type1 and type2 at Phonopy.dataset.
 
-        Parameters
-        ----------
-        v223_mode : bool
-            When True, old dataset yaml format is generated. Default is False.
-
         """
         if dataset is not None:
             if "first_atoms" in dataset:
@@ -669,24 +663,25 @@ class PhonopyYamlDumperBase(ABC):
                     dataset, with_forces=with_forces, key_prefix=key_prefix
                 )
             elif "displacements" in dataset:
-                if v223_mode:
-                    return self._displacements_yaml_lines_type2_v223(
-                        dataset, with_forces=with_forces, key_prefix=key_prefix
-                    )
-                else:
-                    return self._displacements_yaml_lines_type2(
-                        dataset, with_forces=with_forces, key_prefix=key_prefix
-                    )
+                return self._displacements_yaml_lines_type2(
+                    dataset, with_forces=with_forces, key_prefix=key_prefix
+                )
         return []
 
-    @abstractmethod
     def _displacements_yaml_lines_type1(
         self,
         dataset: Type1DisplacementDataset,
         with_forces: bool = False,
         key_prefix: str = "",
     ) -> list[str]:
-        pass
+        """Return type1 dataset in yaml.
+
+        See data structure at Phonopy.dataset.
+
+        """
+        return _displacements_yaml_lines_type1(
+            dataset, with_forces=with_forces, key_prefix=key_prefix
+        )
 
     def _displacements_yaml_lines_type2(
         self,
@@ -725,47 +720,6 @@ class PhonopyYamlDumperBase(ABC):
 
         return lines
 
-    def _displacements_yaml_lines_type2_v223(
-        self,
-        dataset: Type2DisplacementDataset,
-        with_forces: bool = False,
-        key_prefix: str = "",
-    ) -> list[str]:
-        """Return type2 dataset in old stype yaml.
-
-        This is the format < v2.24.
-
-        See data structure at Phonopy.dataset.
-
-        """
-        if "random_seed" in dataset:
-            lines = [
-                "random_seed: %d" % dataset["random_seed"],
-                f"{key_prefix}displacements:",
-            ]
-        else:
-            lines = [
-                f"{key_prefix}displacements:",
-            ]
-        for i, dset in enumerate(dataset["displacements"]):
-            lines.append(f"- # {i + 1}")
-            for j, d in enumerate(dset):
-                lines.append(f"  - displacement: # {j + 1}")
-                lines.append("      [ %20.16f,%20.16f,%20.16f ]" % tuple(d))
-                if with_forces and "forces" in dataset:
-                    f = dataset["forces"][i][j]
-                    lines.append("    force:")
-                    lines.append("      [ %20.16f,%20.16f,%20.16f ]" % tuple(f))
-        lines.append("")
-
-        if "supercell_energies" in dataset:
-            lines.append(f"{key_prefix}supercell_energies:")
-            for i, energy in enumerate(dataset["supercell_energies"]):
-                lines.append(f"- {energy:.8f} # {i + 1}")
-            lines.append("")
-
-        return lines
-
     def _force_constants_yaml_lines(self) -> list[str]:
         lines = []
         if (
@@ -809,18 +763,6 @@ class PhonopyYamlDumper(PhonopyYamlDumperBase):
             symbols = self._data.primitive.symbols
         return self._nac_yaml_lines_given_symbols(symbols)
 
-    def _displacements_yaml_lines_type1(
-        self, dataset: dict, with_forces: bool = False, key_prefix: str = ""
-    ) -> list[str]:
-        """Return type1 dataset in yaml.
-
-        See data structure at Phonopy.dataset.
-
-        """
-        return _displacements_yaml_lines_type1(
-            dataset, with_forces=with_forces, key_prefix=key_prefix
-        )
-
 
 class PhonopyYaml:
     """PhonopyYaml is a container of phonopy setting.
@@ -1213,18 +1155,18 @@ def load_yaml(fp: str | os.PathLike | typing.IO) -> dict:
     lzma and gzip comppressed non-stream files can be loaded.
 
     """
-    if isinstance(fp, io.IOBase):
-        yaml_data = yaml.load(fp, Loader=Loader)
-    else:
+    if isinstance(fp, (str, os.PathLike)):
         myio = get_io_module_to_decompress(fp)
         with myio.open(fp, "rb") as f:
             yaml_data = yaml.load(f, Loader=Loader)
+    else:
+        yaml_data = yaml.load(fp, Loader=Loader)
 
     return yaml_data
 
 
 def _displacements_yaml_lines_type1(
-    dataset: dict, with_forces: bool = False, key_prefix: str = ""
+    dataset: Type1DisplacementDataset, with_forces: bool = False, key_prefix: str = ""
 ) -> list:
     """Return type1 dataset in yaml.
 

{phonopy-3.2.0 → phonopy-3.3.0}/phonopy/phonon/dos.py

@@ -413,8 +413,8 @@ class ProjectedDos(Dos):
     def plot(
         self,
         ax,
-        indices: list[list[int]] | None = None,
-        legend: list[str] | None = None,
+        indices: Sequence[Sequence[int]] | None,
+        legend: Sequence[str] | None = None,
         legend_prop: dict | None = None,
         legend_frameon: bool = True,
         xlabel: str | None = None,
@@ -615,8 +615,8 @@ def plot_projected_dos(
     ax,
     frequency_points: NDArray[np.double],
     projected_dos: NDArray[np.double],
-    indices: list[list[int]] | None = None,
-    legend: list[str] | None = None,
+    indices: Sequence[Sequence[int]] | None = None,
+    legend: Sequence[str] | None = None,
     legend_prop: dict | None = None,
     legend_frameon: bool = True,
     xlabel: str | None = None,

{phonopy-3.2.0 → phonopy-3.3.0}/phonopy/phonon/group_velocity.py

@@ -81,7 +81,7 @@ class GroupVelocity:
 
     def __init__(
         self,
-        dynamical_matrix: DynamicalMatrix | DynamicalMatrixNAC,
+        dynamical_matrix: DynamicalMatrix,
         q_length: float | None = None,
         symmetry: Symmetry | None = None,
         frequency_factor_to_THz: float | None = None,
@@ -89,7 +89,7 @@ class GroupVelocity:
     ) -> None:
         """Init method.
 
-        dynamical_matrix : DynamicalMatrix or DynamicalMatrixNAC
+        dynamical_matrix : DynamicalMatrix
             Dynamical matrix class instance.
         q_length : float
             This is used such as D(q + q_length) - D(q - q_length) for
@@ -107,7 +107,9 @@ class GroupVelocity:
         self._dynmat = dynamical_matrix
         primitive = dynamical_matrix.primitive
         self._reciprocal_lattice_inv = primitive.cell
-        self._reciprocal_lattice = np.linalg.inv(self._reciprocal_lattice_inv)
+        self._reciprocal_lattice: NDArray[np.double] = np.linalg.inv(
+            self._reciprocal_lattice_inv
+        )  # type: ignore
         self._q_length = q_length
         if isinstance(self._dynmat, DynamicalMatrixGL):
             if self._q_length is None:

{phonopy-3.2.0 → phonopy-3.3.0}/phonopy/phonon/modulation.py

@@ -65,7 +65,7 @@ class Modulation:
         phonon_modes: Sequence[tuple[NDArray[np.double], int, float, float]],
         delta_q: NDArray[np.double] | Sequence[float] | None = None,
         derivative_order: int | None = None,
-        nac_q_direction: NDArray[np.double] | None = None,
+        nac_q_direction: Sequence[float] | NDArray[np.double] | None = None,
         factor: float | None = None,
     ) -> None:
         """Init method."""
@@ -74,7 +74,11 @@ class Modulation:
         self._phonon_modes = phonon_modes
         self._dimension = np.array(dimension, dtype="int64").ravel()
         self._delta_q = delta_q
-        self._nac_q_direction = nac_q_direction
+        self._nac_q_direction = (
+            np.array(nac_q_direction, dtype="double")
+            if nac_q_direction is not None
+            else None
+        )
         self._ddm = DerivativeOfDynamicalMatrix(dynamical_matrix)
         self._derivative_order = derivative_order
 

{phonopy-3.2.0 → phonopy-3.3.0}/phonopy/phonon/moment.py

@@ -54,7 +54,7 @@ class PhononMoment:
     def __init__(
         self,
         frequencies: NDArray[np.double],
-        weights: NDArray[np.double],
+        weights: NDArray[np.int64],
         eigenvectors: NDArray[np.cdouble] | None = None,
     ) -> None:
         """Init method."""

{phonopy-3.2.0 → phonopy-3.3.0}/phonopy/phonon/qpoints.py

@@ -93,7 +93,7 @@ class QpointsPhonon:
         | Sequence[NDArray[np.double]]
         | NDArray[np.double],
         dynamical_matrix: DynamicalMatrix | DynamicalMatrixNAC,
-        nac_q_direction: NDArray[np.double] | None = None,
+        nac_q_direction: Sequence[float] | NDArray[np.double] | None = None,
         with_eigenvectors: bool = False,
         group_velocity: GroupVelocity | None = None,
         with_dynamical_matrices: bool = False,
@@ -132,7 +132,11 @@ class QpointsPhonon:
 
         self._qpoints = np.asarray(qpoints, dtype="double", order="C")
         self._dynamical_matrix = dynamical_matrix
-        self._nac_q_direction = nac_q_direction
+        self._nac_q_direction = (
+            np.array(nac_q_direction, dtype="double")
+            if nac_q_direction is not None
+            else None
+        )
         self._with_eigenvectors = with_eigenvectors
         self._gv_obj: GroupVelocity | None = group_velocity
         self._with_dynamical_matrices = with_dynamical_matrices

{phonopy-3.2.0 → phonopy-3.3.0}/phonopy/phonon/thermal_displacement.py

@@ -101,7 +101,7 @@ class ThermalMotion:
         return self._temperatures
 
     @temperatures.setter
-    def temperatures(self, temperatures: NDArray[np.double]) -> None:
+    def temperatures(self, temperatures: Sequence[float] | NDArray[np.double]) -> None:
         t_array = np.array(temperatures, dtype="double")
         condition = np.logical_not(t_array < 0)
         self._temperatures = np.extract(condition, t_array).astype("double")

{phonopy-3.2.0 → phonopy-3.3.0}/phonopy/spectrum/dynamic_structure_factor.py

@@ -36,7 +36,7 @@
 
 from __future__ import annotations
 
-from collections.abc import Callable
+from collections.abc import Callable, Sequence
 from typing import cast
 
 import numpy as np
@@ -106,7 +106,7 @@ class DynamicStructureFactor:
     def __init__(
         self,
         mesh_phonon: Mesh | IterMesh,
-        Qpoints: NDArray[np.double],
+        Qpoints: Sequence[Sequence[float]] | NDArray[np.double],
         T: float,
         atomic_form_factor_func: Callable[[str, float], float] | None = None,
         scattering_lengths: dict[str, float] | None = None,

{phonopy-3.2.0 → phonopy-3.3.0}/phonopy/version.py

@@ -34,4 +34,4 @@
 # ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
 # POSSIBILITY OF SUCH DAMAGE.
 
-__version__ = "3.2.0"
+__version__ = "3.3.0"

phonopy-3.2.0/phonopy/_version.py

@@ -1,34 +0,0 @@
-# file generated by setuptools-scm
-# don't change, don't track in version control
-
-__all__ = [
-    "__version__",
-    "__version_tuple__",
-    "version",
-    "version_tuple",
-    "__commit_id__",
-    "commit_id",
-]
-
-TYPE_CHECKING = False
-if TYPE_CHECKING:
-    from typing import Tuple
-    from typing import Union
-
-    VERSION_TUPLE = Tuple[Union[int, str], ...]
-    COMMIT_ID = Union[str, None]
-else:
-    VERSION_TUPLE = object
-    COMMIT_ID = object
-
-version: str
-__version__: str
-__version_tuple__: VERSION_TUPLE
-version_tuple: VERSION_TUPLE
-commit_id: COMMIT_ID
-__commit_id__: COMMIT_ID
-
-__version__ = version = '3.2.0'
-__version_tuple__ = version_tuple = (3, 2, 0)
-
-__commit_id__ = commit_id = 'gd443de28b'